Kondo Hiroko X, Kanematsu Yusuke, Masumoto Gen, Takano Yu
School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan.
Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan.
Database (Oxford). 2020 Oct 1;2023. doi: 10.1093/database/baaa066.
Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure-function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function. Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/.
血红素参与多种生物学功能，如氧气运输、电子传递、氧还原、转录调控等。虽然针对许多血红素蛋白，每种功能的机制都已得到研究，但血红素功能多样性的起源仍不清楚，这是一个关键的科学问题。我们构建了一个血红素蛋白数据库，名为基于Python的血红素卟啉畸变数据库及分析器（PyDISH），它还包含一些分析工具。PyDISH的目的是整合血红素和血红素蛋白的结构信息以及血红素蛋白的功能。该数据库将提供聚焦于血红素卟啉畸变的结构 - 功能关系，并有助于阐明血红素蛋白功能多样性的起源。此外，从该数据库获得的见解可用于蛋白质功能的设计。PyDISH包含从蛋白质数据库中提取的13000多个血红素的结构数据，包括血红素卟啉畸变、与血红素配位的轴向配体以及血红素丙酸侧链的取向。PyDISH还拥有关于蛋白质结构域的信息，包括通用蛋白质资源数据库登录号、基于CATH分类法的蛋白质折叠类型、生物体、配位距离等。PyDISH中实现的分析工具允许用户不仅浏览和下载数据，还能使用PyDISH中实现的分析工具分析血红素卟啉的结构。PyDISH的用户将能够将获得的结果用于蛋白质功能的设计。数据库网址：http://pydish.bio.info.hiroshima-cu.ac.jp/ 。
